Sentences with word «pyrosequencing»

Here we use pyrosequencing of the bacterial 16S rRNA gene to quantify bacterial taxa [21].

Services include: consultation with investigators to chose the best method of analysis; sample preparation, assay design and processing of the most used methods to study DNA methylation, both gene - specific and genome - wide (PyroMeth, RRBS and Methyl - Seq); and assessment of global DNA methylation by pyrosequencing methylation analysis of repetitive elements (LINE - 1 and Alu repeats).

Pyrosequencing using the 454 / Roche GS FLX chemistry was carried out according to the manufacturer's instructions.

The team employed a new, massively parallel technique called pyrosequencing, which uses pulses of light to read the sequence of thousands of bases at once.

Because < 20 % of all gastrointestinal bacteria can be cultured using conventional methodologies, we performed massively parallel pyrosequencing to further assess the qualitative changes in the intestinal microbiome following alcohol exposure.

Work scheme to isolate the different microorganisms found in hydrogen - producing reactors: A study of effectiveness by pyrosequencing analysis — Laura Fuentes — Journal of Applied Microbiology

A Sanger / pyrosequencing hybrid approach for the generation of high - quality draft assemblies of...

One question in analyzing microbial communities by 16S rRNA gene pyrosequencing centers on whether the amplification and sequencing methods result in recovery of sequences in proportion to their representation in the original community [24].

Comparative Analysis of the Gut Bacterial Community of Four Anastrepha Fruit Flies (Diptera: Tephritidae) Based on Pyrosequencing — Carmen Ventura — Current Microbiology

Purified amplicon DNAs were quantified using Quant - iT PicoGreen kit (cat # P7589, Invitrogen, Carlsbad, CA) and pooled for pyrosequencing.

Pääbo and his Leipzig colleague Ed Green also employed pyrosequencing and computers to pick out Neandertal DNA.

CXCR4 pyrosequencing data were assigned to samples by DNA barcode.

Next, background pyrosequencing error, identified by an untransduced control sample, was subtracted from each group of reads.

Amplicons were sequenced on a multiplexed 454 - FLX - Titanium pyrosequencing run at the Human Genome Sequencing center at Baylor College of Medicine.

DNA samples are prepared from microbial specimens, and then analyzed using massively parallel sequencing methods such as 454 / Roche pyrosequencing [20].

Application of high - throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area — A pilot study — Daleniece Higgins — Food Research International

Unfortunately, indels are both the strength and the weakness of 454 data — due to the underlying pyrosequencing, homopolymeric regions are often under - or over-called, resulting in numerous false positives.

We investigated the distal gut bacterial communities of three healthy humans before and after treatment with ciprofloxacin, obtaining more than 7,000 full - length rRNA sequences and over 900,000 pyrosequencing reads from two hypervariable regions of the rRNA gene.

Computer simulations by Liu et al. [43], Wang et al. [41], and Sundquist et al. [47] have indicated that pyrosequencing tags from different regions of the gene will vary in their utility for the distinct tasks of revealing microbial diversity and performing taxonomic classification, both of which contribute to making informative comparisons between complex microbial communities.

Microbial DNA from colon specimens were isolated and analyzed by use of 454 pyrosequencing of 16S RNA genes.

Pbo's group used a technique developed by Branford, Conn. - based biotech company 454 Life Sciences called pyrosequencing, which takes advantage of the fact that ancient DNA is often fragmented.

The exact number of bases in a homopolymeric stretch becomes difficult to resolve by pyrosequencing, and as a result, 454 sequencing tends to overcall or undercall bases in these regions.

454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber.

A Sanger / pyrosequencing hybrid approach for the generation of high - quality draft assemblies of marine microbial genomes.

Pyrosequencing using the Titanium method was carried out using the Titanium genomic kit.

Archaeal community composition in the sediments was analyzed with high - throughput 16S rRNA gene pyrosequencing.

Pyrosequencing, a specialized technique which enables large scale DNA sequencing was employed that helped in detecting so many organisms in a short time.

One commercially available alternative is pyrosequencing, which also detects nucleotides as they are added to a single strand of DNA, but it can lead to errors because it is harder to differentiate between a single base and a whole stretch of identical bases next to each other, says Elaine Mardis, a geneticist at Washington University in St Louis, US.

The recent introduction of the pyrosequencing - based 454 sequencing platform (454 Life Sciences, Branford, CT) offers a very promising sequencing technology alternative for incorporation in WGS.

Given the nature of pyrosequencing, this was not the best idea.

The facility's infrastructure includes a pyrosequencing genetic analyser (PyroMark ID MA) capable of quick and efficient SNP analysis of as many as 480 samples per day, in addition to all the necessary equipment for a more conventional microsatellite genotypic analysis.

Sample processing, 16S rRNA gene amplification, and 454 pyrosequencing was performed following protocols benchmarked as part of the Human Microbiome Project [33], [34].

Using pyrosequencing to determine mtDNA carryover they found that using frozen rather than fresh eggs leads to higher carryover.

By contrast with some other sequencing technologies, which have a high rate of within - read indels (most single molecule sequencing and pyrosequencing - based methods have this attribute), the intra-read gaps in Complete Genomics data are relatively easy to handle.

In this project, we seek to combine modern techniques in a systems biology approach using species - specific in vivo labeling tools (monoclonal antibodies and fluorescent protein - expressing bacteria), monitoring of acid production (pH - sensitive dyes, fluorescent proteins and metabolite profiling), as well as ecology based approaches such as labeling of acid active species with stable isotope probing (SIP) combined with deep 16S rRNA pyrosequencing.

Sogin and his co-workers have demonstrated the power of pyrosequencing by amplifying the V6 variable region of 16S rRNA from marine deep water and hydrothermal vent samples, analyzing over 900,000 bacterial and archaeal tags from the vent system and revealing greater taxonomic richness (over 20,000 OTUs observed at 3 % sequence divergence) than has previously been reported for any microbial habitat [39,42,43].

In the current study, Dethlefsen and his team used a technique called pyrosequencing to take a microbial head count from the stool samples of study participants before they took a short course of ciprofloxacin; then researchers took four more samples over the following eight months.

The researchers then analyzed the types of bacteria present in each sample using a technique called 454 pyrosequencing.

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo - oligosaccharides (FOS) and inulin using high - throughput 454 - pyrosequencing

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